PDBsum entry 1ykp

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
Protein chains
(+ 0 more) 200 a.a. *
(+ 0 more) 238 a.a. *
DHB ×6
_FE ×6
Waters ×786
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Protocatechuate 3,4-dioxygenase y408h mutant bound to dhb
Structure: Protocatechuate 3,4-dioxygenase alpha chain. Chain: a, c, e, g, i, k. Synonym: 3,4-pcd. Engineered: yes. Protocatechuate 3,4-dioxygenase beta chain. Chain: b, d, f, h, j, l. Synonym: 3,4-pcd. Engineered: yes. Mutation: yes
Source: Pseudomonas putida. Organism_taxid: 303. Gene: pcag. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: pcah. Expression_system_taxid: 562
Biol. unit: 24mer (from PDB file)
2.41Å     R-factor:   0.145     R-free:   0.211
Authors: C.K.Brown,D.H.Ohlendorf
Key ref:
M.P.Valley et al. (2005). Roles of the equatorial tyrosyl iron ligand of protocatechuate 3,4-dioxygenase in catalysis. Biochemistry, 44, 11024-11039. PubMed id: 16101286 DOI: 10.1021/bi050902i
18-Jan-05     Release date:   16-Aug-05    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P00436  (PCXA_PSEPU) -  Protocatechuate 3,4-dioxygenase alpha chain
201 a.a.
200 a.a.
Protein chains
Pfam   ArchSchema ?
P00437  (PCXB_PSEPU) -  Protocatechuate 3,4-dioxygenase beta chain
239 a.a.
238 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L: E.C.  - Protocatechuate 3,4-dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Benzoate Metabolism
      Reaction: 3,4-dihydroxybenzoate + O2 = 3-carboxy-cis,cis-muconate
Bound ligand (Het Group name = DHB)
corresponds exactly
+ O(2)
= 3-carboxy-cis,cis-muconate
      Cofactor: Iron
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     catalytic activity     8 terms  


DOI no: 10.1021/bi050902i Biochemistry 44:11024-11039 (2005)
PubMed id: 16101286  
Roles of the equatorial tyrosyl iron ligand of protocatechuate 3,4-dioxygenase in catalysis.
M.P.Valley, C.K.Brown, D.L.Burk, M.W.Vetting, D.H.Ohlendorf, J.D.Lipscomb.
The active site Fe(III) of protocatechuate 3,4-dioxygenase (3,4-PCD) from Pseudomonas putida is ligated axially by Tyr447 and His462 and equatorially by Tyr408, His460, and OH(-). Tyr447 and OH(-) are displaced as protocatechuate (3,4-dihydroxybenzoate, PCA) chelates the iron and appear to serve as in situ bases to promote this process. The role(s) of Tyr408 is (are) explored here using mutant enzymes that exhibit less than 0.1% wild-type activity. The X-ray crystal structures of the mutants and their PCA complexes show that the new shorter residues in the 408 position cannot ligate the iron and instead interact with the iron through solvents. Moreover, PCA binds as a monodentate rather than a bidentate ligand, and Tyr447 fails to dissociate. Although the new residues at position 408 do not directly bind to the iron, large changes in the spectroscopic and catalytic properties are noted among the mutant enzymes. Resonance Raman features show that the Fe-O bond of the monodentate 4-hydroxybenzoate (4HB) inhibitor complex is significantly stronger in the mutants than in wild-type 3,4-PCD. Transient kinetic studies show that PCA and 4HB bind to 3,4-PCD in a fast, reversible step followed by a step in which coordination to the metal occurs; the latter process is at least 50-fold slower in the mutant enzymes. It is proposed that, in wild-type 3,4-PCD, the Lewis base strength of Tyr408 lowers the Lewis acidity of the iron to foster the rapid exchange of anionic ligands during the catalytic cycle. Accordingly, the increase in Lewis acidity of the iron caused by substitution of this residue by solvent tends to make the iron substitution inert. Tyr447 cannot be released to allow formation of the usual dianionic PCA chelate complex with the active site iron, and the rate of electrophilic attack by O(2) becomes rate limiting overall. The structures of the PCA complexes of these mutant enzymes show that hydrogen-bonding interactions between the new solvent ligand and the new second-sphere residue in position 408 allow this residue to significantly influence the spectroscopic and kinetic properties of the enzymes.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21246129 N.Anitha, and M.Palaniandavar (2011).
Mononuclear iron(III) complexes of 3N ligands in organized assemblies: spectral and redox properties and attainment of regioselective extradiol dioxygenase activity.
  Dalton Trans, 40, 1888-1901.  
20835480 R.Mayilmurugan, M.Sankaralingam, E.Suresh, and M.Palaniandavar (2010).
Novel square pyramidal iron(III) complexes of linear tetradentate bis(phenolate) ligands as structural and reactive models for intradiol-cleaving 3,4-PCD enzymes: Quinone formation vs. intradiol cleavage.
  Dalton Trans, 39, 9611-9625.  
17256852 M.Y.Pau, M.I.Davis, A.M.Orville, J.D.Lipscomb, and E.I.Solomon (2007).
Spectroscopic and electronic structure study of the enzyme-substrate complex of intradiol dioxygenases: substrate activation by a high-spin ferric non-heme iron site.
  J Am Chem Soc, 129, 1944-1958.  
17031705 R.F.Abdelhamid, Y.Obara, Y.Uchida, T.Kohzuma, D.M.Dooley, D.E.Brown, and H.Hori (2007).
Pi-pi interaction between aromatic ring and copper-coordinated His81 imidazole regulates the blue copper active-site structure.
  J Biol Inorg Chem, 12, 165-173.  
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